I understand that one of the main causes of failure in the V6 transmissions is heat. My fluid is brownish red with a light burnt odor (the tranny has no problems though) so I was going to replace that anyways. While I was at it, I decided on adding a standalone transmission cooler. I had a couple questions though.

Should I use this instead of or in conjunction with the radiator's cooler?
Should I get the fluid flushed and completely refilled, or should a drain and refill be sufficient?

I live in the northeast, so temps vary from up to 90F in the summer to as low as -18F in the winter.

 

It is used only to supplement the radiator. You never EVER flush a Honda automatic transmission. Just drain and fills with driving in between to help circulate the new fluid through the tranny to dilute out the old. You drain and fill, drive ten miles, check fluid. If it's not red yet, drain and fill, drive ten miles, til the fluid is red after driving. Only use Honda atf. When you drain and fill, buy two gallon jugs, drain the old into a jug. Pour new fluid into the other jug until the amount is the same on a level surface.

 

You want to maintain the in radiator cooler with an auxiliary cooler. With colder climates with just the stand alone cooler it is possible to overcool the trans fluid.

 

So if it's used in conjunction with the radiator, do I still need to make sure the auxillilary has a bypass?

 

Bypass, no.
Just place it in series with the rad cooler.